CiteULike | Further Information

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Mendeley | Further Information

{"title"=>"Genome features of \"dark-fly\", a drosophila line reared long-term in a dark environment", "type"=>"journal", "authors"=>[{"first_name"=>"Minako", "last_name"=>"Izutsu", "scopus_author_id"=>"55276196800"}, {"first_name"=>"Jun", "last_name"=>"Zhou", "scopus_author_id"=>"56908579700"}, {"first_name"=>"Yuzo", "last_name"=>"Sugiyama", "scopus_author_id"=>"55277573600"}, {"first_name"=>"Osamu", "last_name"=>"Nishimura", "scopus_author_id"=>"55729138600"}, {"first_name"=>"Tomoyuki", "last_name"=>"Aizu", "scopus_author_id"=>"6506762294"}, {"first_name"=>"Atsushi", "last_name"=>"Toyoda", "scopus_author_id"=>"55488478100"}, {"first_name"=>"Asao", "last_name"=>"Fujiyama", "scopus_author_id"=>"7003611650"}, {"first_name"=>"Kiyokazu", "last_name"=>"Agata", "scopus_author_id"=>"7005905990"}, {"first_name"=>"Naoyuki", "last_name"=>"Fuse", "scopus_author_id"=>"7003376749"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84863244338", "pui"=>"364433956", "sgr"=>"84863244338", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "issn"=>"19326203", "pmid"=>"22432011", "doi"=>"10.1371/journal.pone.0033288"}, "id"=>"60561848-071a-3f71-88e6-7f764c7d0148", "abstract"=>"Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed \"Dark-fly\", which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.", "link"=>"http://www.mendeley.com/research/genome-features-darkfly-drosophila-line-reared-longterm-dark-environment", "reader_count"=>145, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>10, "Researcher"=>35, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>5, "Student > Master"=>21, "Other"=>6, "Student > Bachelor"=>21, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>10, "Researcher"=>35, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>5, "Student > Master"=>21, "Other"=>6, "Student > Bachelor"=>21, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Biochemistry, Genetics and Molecular Biology"=>17, "Agricultural and Biological Sciences"=>106, "Medicine and Dentistry"=>1, "Neuroscience"=>5, "Arts and Humanities"=>1, "Design"=>1, "Psychology"=>6, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>5}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>6}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>106}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Romania"=>1, "United States"=>6, "Japan"=>4, "United Kingdom"=>2, "Portugal"=>1, "India"=>1, "Canada"=>1, "Austria"=>1, "China"=>1, "Brazil"=>4, "Italy"=>1, "Chile"=>2, "France"=>1, "Germany"=>1}, "group_count"=>2}

ORCID

CrossRef

• http://doi.org/10.1128/AEM.03973-14
• http://doi.org/10.1111/1755-0998.12107
• http://doi.org/10.1038/nature.2016.19339
• http://doi.org/10.1111/phen.12158
• http://doi.org/10.1038/srep37923
• http://doi.org/10.1093/icb/icv100
• http://doi.org/10.1038/nrg3564
• http://doi.org/10.1038/s41598-017-07461-9
• http://doi.org/10.1128/JVI.01127-14
• http://doi.org/10.1080/09291016.2019.1581480
• http://doi.org/10.1080/09291016.2017.1345426
• http://doi.org/10.1085/jgp.201812107
• http://doi.org/10.1534/g3.115.023549
• http://doi.org/10.1016/j.physbeh.2014.02.015
• http://doi.org/10.1016/j.etap.2014.11.024
• http://doi.org/10.1016/j.gde.2017.03.004
• http://doi.org/10.1080/00987913.2014.947839

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{"UNIPROT"=>547}

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• 4357955
• 4178783
• 4239992

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• {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%252Fjournal.pone.0033288", "share_count"=>0, "like_count"=>0, "comment_count"=>0, "click_count"=>0, "total_count"=>0}

Journal Comments | Further Information

• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/82bffb7f-7aa0-4c8b-b7dd-bbf32205ef14", "title"=>"Original \"Dark Fly\" paper published over 100 years ago not cited here", "body"=>"I find it very odd that this work does not cite Fernandus Payne's classic 1910 paper in the Biological Bulletin entitled \"Forty-nine Generations in the Dark\" which performed essentially the same experiment in order to test Lamarkian evolution, especially given that this project is widely known to be instrumental in T.H. Morgan's choice to focus on ''Drosophila melanogaster'' as a model organism for research in genetics.\n\nSee the original paper here: http://www.biolbull.org/content/18/4/188.full.pdf+html\n\nSee also a discussion of the role of the original \"Dark Fly\" experiment on the history of Genetics here: http://www.jstor.org/stable/228840 \n\n", "isRemoved"=>false, "created"=>"2012-03-19T16:38:07Z", "lastModified"=>"2012-03-19T16:38:07Z", "creator"=>{"userId"=>"20801"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0033288", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2012-05-08T11:44:40Z", "replies"=>[{"type"=>"REPLY", "parentID"=>11925, "annotationUri"=>"info:doi/10.1371/reply/dad86ed6-98c6-4c75-bc1d-600f93a6aca6", "title"=>"RE: Original \"Dark Fly\" paper published over 100 years ago not cited here", "body"=>"Thank you for your comment. We did not cite the historical references, but Mori, who started to rear Dark-fly, discussed about the Payne’s works in his paper (see Mori, 1986). Although these previous studies mainly focus on the traits selected in dark conditions, we focus on the genome alterations involved in the adaptation. Therefore, we mainly discussed about molecular studies of the naturally and laboratory evolved organisms. I also note that our Dark-fly has been reared for 1400 generations longer than the Payne’s fly. I appreciate you to remind us the position of our work on the history of Drosophila research.\nNaoyuki Fuse\n", "isRemoved"=>false, "created"=>"2012-05-08T11:44:40Z", "lastModified"=>"2012-05-08T11:44:40Z", "creator"=>{"userId"=>"268219"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0033288", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-05-08T11:44:40Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/af6cdcbc-8a91-4747-90b1-2997a1d5c76f", "title"=>"Media Coverage of This Article", "body"=>"The following represents some of the media coverage that has occurred for this paper:\n\nPublication: Reddit \nTitle: “A fly species was kept in complete darkness for 57 years (1400 generations), showing genetic alterations that occur as a result of environmental conditions. : science”\nhttp://www.reddit.com/r/science/comments/r2wkz/a_fly_species_was_kept_in_complete_darkness_for\n\nIf you see any additional coverage of this paper in the press or blogosphere, please reply to this thread and add the link to the article. \n", "isRemoved"=>false, "created"=>"2012-03-23T20:37:35Z", "lastModified"=>"2012-03-23T20:37:35Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"PLoS ONE Staff"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0033288", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-03-23T20:37:35Z", "replies"=>[]}

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Twitter

• {"id"=>"203505149124157443", "text"=>"Evrim teorisi ve doğal seçilime dair sıkıntıları olanlara güncel referanslarla gelen ilaç gibi makale: http://t.co/MVUynR0e (via @selimok).", "created_at"=>"2012-05-18T15:19:43Z", "user"=>"merenbey", "user_name"=>"A. Murat Eren", "user_profile_image"=>"http://a0.twimg.com/profile_images/1532062283/irene-15_normal.jpg"}
• {"id"=>"265477662322089985", "text"=>"My brother sent me this. This too is genetics, but can't help but feel sorry for them flies #PLOSONE: http://t.co/Dsx5dG6n", "created_at"=>"2012-11-05T15:36:21Z", "user"=>"kristienhens", "user_name"=>"Kristien Hens", "user_profile_image"=>"http://a0.twimg.com/profile_images/1424410568/Kristien_002_normal.jpg"}
• {"id"=>"271332353199181824", "text"=>"Un ejemplo más tangible: experimento de 57 años sobre evolución en Drosophila: http://t.co/6fXCBvFD\nResumen: http://t.co/TTnOf9Gf ;)", "created_at"=>"2012-11-21T19:20:48Z", "user"=>"MGragera", "user_name"=>"Marcos Gragera", "user_profile_image"=>"http://a0.twimg.com/profile_images/1501859728/fototwitter_normal.png"}
• {"id"=>"271341489471246336", "text"=>"RT @MGragera: Un ejemplo más tangible: experimento de 57 años sobre evolución en Drosophila: http://t.co/6fXCBvFD\nResumen: http://t.co/T ...", "created_at"=>"2012-11-21T19:57:07Z", "user"=>"SGJ93", "user_name"=>"Sergio G. Jiménez", "user_profile_image"=>"http://a0.twimg.com/profile_images/2714843563/8a64f5f3645e43392a13ee2a8632d1b8_normal.jpeg"}
• {"id"=>"271351175507484673", "text"=>"RT @MGragera: Un ejemplo más tangible: experimento de 57 años sobre evolución en Drosophila: http://t.co/6fXCBvFD\nResumen: http://t.co/T ...", "created_at"=>"2012-11-21T20:35:36Z", "user"=>"BorjaSugar", "user_name"=>"Borja Sugar", "user_profile_image"=>"http://a0.twimg.com/profile_images/2710448497/6d63e83c26980b4db857ace713cd6472_normal.jpeg"}
• {"id"=>"276949627398402048", "text"=>"Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment http://t.co/9sVakeF0", "created_at"=>"2012-12-07T07:21:51Z", "user"=>"hal_spiral", "user_name"=>"遼季", "user_profile_image"=>"http://a0.twimg.com/profile_images/1267438106/twipple1299727097815_normal.jpg"}
• {"id"=>"278030056788488192", "text"=>"Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment http://t.co/s2JZbddP", "created_at"=>"2012-12-10T06:55:05Z", "user"=>"an_emerald", "user_name"=>"アッコ", "user_profile_image"=>"http://a0.twimg.com/profile_images/1188414476/DVC00299_bigger_normal.JPG"}
• {"id"=>"287234722877300736", "text"=>"Flies kept in darkness for 57 years (1400 generations) - the results indicate evolution. #science #2012 http://t.co/ba2JJlr5", "created_at"=>"2013-01-04T16:31:09Z", "user"=>"almirathunstrom", "user_name"=>"almira thunström", "user_profile_image"=>"http://a0.twimg.com/profile_images/3056589296/b867764f92cce8896d9baa60674166e8_normal.jpeg"}
• {"id"=>"287305115185074176", "text"=>"RT @almirathunstrom Flies kept in dark for 57 years (1400 generations) - the results indicate evolution. #science #2012 http://t.co/oX9P9PyM", "created_at"=>"2013-01-04T21:10:51Z", "user"=>"ChrisClegg80", "user_name"=>"Chris Clegg", "user_profile_image"=>"http://a0.twimg.com/profile_images/2652985190/1c2a61473a9c999cd72ef95481d7ee4a_normal.png"}
• {"id"=>"288014838263869442", "text"=>"@friendsofdarwin help in answering ape question. Flies kept in dark for 57 years (1400 generations), altered. http://t.co/wOUIpyRJ", "created_at"=>"2013-01-06T20:11:03Z", "user"=>"almirathunstrom", "user_name"=>"almira thunström", "user_profile_image"=>"http://a0.twimg.com/profile_images/3056589296/b867764f92cce8896d9baa60674166e8_normal.jpeg"}
• {"id"=>"288015928535437314", "text"=>"@friendsofdarwin sorry the real link; not apes but mechanism of gene selection and species co-existing with same origin http://t.co/YCWVi2mm", "created_at"=>"2013-01-06T20:15:23Z", "user"=>"almirathunstrom", "user_name"=>"almira thunström", "user_profile_image"=>"http://a0.twimg.com/profile_images/3056589296/b867764f92cce8896d9baa60674166e8_normal.jpeg"}
• {"id"=>"290519876609638400", "text"=>"What happens when a \"dark fly\" and Oregon-R-S strain mate? Would they? Looking forward to the answers #evolution. http://t.co/ba2JJlr5", "created_at"=>"2013-01-13T18:05:10Z", "user"=>"almirathunstrom", "user_name"=>"almira thunström", "user_profile_image"=>"http://a0.twimg.com/profile_images/3056589296/b867764f92cce8896d9baa60674166e8_normal.jpeg"}
• {"id"=>"392419711478030336", "text"=>"@LogicRottweiler http://t.co/b0jzEc7khk ...limited genetic adaptions for entropy, not evolution. Did they grow a flashlight? No.", "created_at"=>"2013-10-21T22:38:44Z", "user"=>"yaboynov", "user_name"=>"Aaron Novikoff", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3696930577/f9471bb117ae86a13528fa13aa113951_normal.jpeg"}
• {"id"=>"392642043333595136", "text"=>"RT @yaboynov: @LogicRottweiler http://t.co/b0jzEc7khk ...limited genetic adaptions for entropy, not evolution. Did they grow a flashlight…", "created_at"=>"2013-10-22T13:22:12Z", "user"=>"TakeThatDarwin", "user_name"=>"Take That Darwin", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000578210067/1966b9c63b39ad4d083475b356595f74_normal.png"}
• {"id"=>"412954690955907072", "text"=>"↓2012年3月の記事。変化してる解毒代謝遺伝子はUGT遺伝子なんかか。 http://t.co/xpW186oQWA", "created_at"=>"2013-12-17T14:37:25Z", "user"=>"fiddler_K", "user_name"=>"Kawai_Yusuke", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1178308026/IMGP0358_normal.JPG"}
• {"id"=>"429667670699425792", "text"=>"@AtyHans dna change has limitations of functionality. What is 'positive' is an available adaption, not a new feature. http://t.co/b0jzEc7khk", "created_at"=>"2014-02-01T17:28:50Z", "user"=>"yaboynov", "user_name"=>"Aaron Novikoff", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3696930577/f9471bb117ae86a13528fa13aa113951_normal.jpeg"}
• {"id"=>"430901937974702080", "text"=>"@AtheistDan_ there is a reason we don't have six fingers. Highly encourage you to look at this study http://t.co/nOrnw8Z6fg but adaption", "created_at"=>"2014-02-05T03:13:22Z", "user"=>"yaboynov", "user_name"=>"Aaron Novikoff", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3696930577/f9471bb117ae86a13528fa13aa113951_normal.jpeg"}
• {"id"=>"430903702732275712", "text"=>"@AtheistDan_ http://t.co/b0jzEc7khk", "created_at"=>"2014-02-05T03:20:23Z", "user"=>"yaboynov", "user_name"=>"Aaron Novikoff", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3696930577/f9471bb117ae86a13528fa13aa113951_normal.jpeg"}
• {"id"=>"448866577690419201", "text"=>"What happens when you leave flies in the dark for 58 years: http://t.co/oxJIoCyUFk", "created_at"=>"2014-03-26T16:58:26Z", "user"=>"Achifaifa", "user_name"=>"Yuri Numerov", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1229014594/miavatar100PS_normal.png"}
• {"id"=>"448921017755250688", "text"=>"http://t.co/WfA9TWVc4M Cool article on adaptation.", "created_at"=>"2014-03-26T20:34:45Z", "user"=>"khloestarr", "user_name"=>"khloe morris", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2911453586/66b572d50e075503cad29ef6c0fdea90_normal.jpeg"}
• {"id"=>"448965410504077312", "text"=>"@neiltyson Fruit flies kept in complete darkness for 57 years (1400 generations), showing genetic alterations http://t.co/waA7CvwO4h", "created_at"=>"2014-03-26T23:31:09Z", "user"=>"poet8061", "user_name"=>"David Santamaria", "user_profile_image"=>"http://pbs.twimg.com/profile_images/412297742229061632/UI8MwclB_normal.jpeg"}
• {"id"=>"448971968499699713", "text"=>"Link pros interessados: http://t.co/PFpp3ByCKW", "created_at"=>"2014-03-26T23:57:13Z", "user"=>"vladschuler", "user_name"=>"Vlad Schüler", "user_profile_image"=>"http://pbs.twimg.com/profile_images/447399302814371840/wPvSSYOt_normal.png"}
• {"id"=>"448974185855852544", "text"=>"@OxyEvo fruit flies kept in complete darkness for 1400 generations (57 years), exhibit genetic alterations\nhttp://t.co/dGEwK8uss9", "created_at"=>"2014-03-27T00:06:02Z", "user"=>"CamSprenger", "user_name"=>"CamSprenger", "user_profile_image"=>"http://pbs.twimg.com/profile_images/428044341458649089/qw0m5kH6_normal.jpeg"}
• {"id"=>"448976580266979328", "text"=>"A species of fruit fly was kept in darkness for 57 yrs; genetic mutations thrived. IOW, natural selection. http://t.co/QElJ6UHN4M", "created_at"=>"2014-03-27T00:15:32Z", "user"=>"bradydan", "user_name"=>"Dan Brady", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1268735695/Dan-crop_normal.jpg"}
• {"id"=>"448977209437339648", "text"=>"@jploenneke So say my descendants didn't leave the gym... Like ever. Similar situation?\n\nhttp://t.co/N10fn74XTH", "created_at"=>"2014-03-27T00:18:02Z", "user"=>"Hetvler", "user_name"=>"King Conrad", "user_profile_image"=>"http://pbs.twimg.com/profile_images/444214621994373120/8ZObHFh3_normal.jpeg"}
• {"id"=>"448978481402355712", "text"=>"Evolution +can+ be studied experimentally, and it's super fascinating! Fruit flies kept in the dark for 57yrs: http://t.co/hXtTHVu8Dl", "created_at"=>"2014-03-27T00:23:06Z", "user"=>"johnleach", "user_name"=>"John Leach", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3458734603/55724162c14cb41ce6c0ae219a6656c2_normal.jpeg"}
• {"id"=>"449030920159240192", "text"=>"They kept a species of fruit fly in the dark for 57 years (1400 generations); here is what they found http://t.co/OpaQBIh6wI", "created_at"=>"2014-03-27T03:51:28Z", "user"=>"sesquiotic", "user_name"=>"James Harbeck", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000402975657/904063f0edf0f13dc87d89563ffa0569_normal.jpeg"}
• {"id"=>"449034586765664256", "text"=>"It's evolution home skillet. - http://t.co/Tuk8faG3vc", "created_at"=>"2014-03-27T04:06:02Z", "user"=>"brodybeck", "user_name"=>"Brody Beck", "user_profile_image"=>"http://pbs.twimg.com/profile_images/446646593341513728/6wbNfYHk_normal.jpeg"}
• {"id"=>"449036738850455552", "text"=>"RT @sesquiotic: They kept a species of fruit fly in the dark for 57 years (1400 generations); here is what they found http://t.co/OpaQBIh6wI", "created_at"=>"2014-03-27T04:14:35Z", "user"=>"43n79w", "user_name"=>"Paul Jara", "user_profile_image"=>"http://pbs.twimg.com/profile_images/441725332320555008/24qHclgT_normal.jpeg"}
• {"id"=>"449060430762487808", "text"=>"RT @johnleach: Evolution +can+ be studied experimentally, and it's super fascinating! Fruit flies kept in the dark for 57yrs: http://t.co/h…", "created_at"=>"2014-03-27T05:48:44Z", "user"=>"terryjackman", "user_name"=>"Terry Jackman", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2454653092/terryjackman_normal.jpg"}
• {"id"=>"449183206139781120", "text"=>"a study on evolution. They kept a bunchof flies quarantined in a dark environment for, get ready..57YEARS (1400 Gens) http://t.co/d4MATVlqPJ", "created_at"=>"2014-03-27T13:56:36Z", "user"=>"CharlesTheForth", "user_name"=>"Charles Lloyd IV", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1881640227/me_normal.jpg"}
• {"id"=>"449252551037173760", "text"=>"http://t.co/WcfNLcUZQu @benji_mundo this evidence for evolution doeeee", "created_at"=>"2014-03-27T18:32:09Z", "user"=>"keshawnswaqqboi", "user_name"=>"Jesus H. Christ", "user_profile_image"=>"http://pbs.twimg.com/profile_images/436248009030905856/7dPxayIj_normal.jpeg"}
• {"id"=>"449253292833783808", "text"=>"RT @keshawnswaqqboi: http://t.co/WcfNLcUZQu @benji_mundo this evidence for evolution doeeee", "created_at"=>"2014-03-27T18:35:06Z", "user"=>"benji_mundo", "user_name"=>"Ben", "user_profile_image"=>"http://pbs.twimg.com/profile_images/448974165744558081/6rgBcl3K_normal.jpeg"}
• {"id"=>"449407733939580928", "text"=>"RT @sesquiotic: They kept a species of fruit fly in the dark for 57 years (1400 generations); here is what they found http://t.co/OpaQBIh6wI", "created_at"=>"2014-03-28T04:48:48Z", "user"=>"maxbaru", "user_name"=>"Maksim Baru", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1828395631/28472_405932873359_505758359_4203480_2530056_n_normal.jpg"}
• {"id"=>"450561140666290177", "text"=>"#PLOSONE: Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment http://t.co/Iry3RhUTDn", "created_at"=>"2014-03-31T09:12:01Z", "user"=>"Franck_who", "user_name"=>"Franck Touret", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3451452430/6b93ede7d271a65a6064d22609a75d2e_normal.jpeg"}
• {"id"=>"451924052559806464", "text"=>"more proof of evolution for the non-believers http://t.co/fGJQXj3Buf", "created_at"=>"2014-04-04T03:27:45Z", "user"=>"garren296", "user_name"=>"air canada", "user_profile_image"=>"http://pbs.twimg.com/profile_images/446837330729787392/dsWNSVla_normal.jpeg"}
• {"id"=>"452113945138954240", "text"=>"flies grown in the dark for 57 years. whoa. http://t.co/Kpj2C1oNTG", "created_at"=>"2014-04-04T16:02:19Z", "user"=>"feuerwachter", "user_name"=>"Fernando Santiago", "user_profile_image"=>"http://pbs.twimg.com/profile_images/432861371214991361/sWH6af2S_normal.jpeg"}
• {"id"=>"485257683570655232", "text"=>"@DarkMatter2525 Evolution of Dark-Fly http://t.co/GndZxf7Hgl", "created_at"=>"2014-07-05T03:03:42Z", "user"=>"DonaldKronos", "user_name"=>"Donald Kronos *Actor", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1293561846/30_normal.jpg"}
• {"id"=>"519575070042095616", "text"=>"http://t.co/AjnemfkiBn", "created_at"=>"2014-10-07T19:48:44Z", "user"=>"LSF142_Saul", "user_name"=>"Saul Jonas", "user_profile_image"=>"http://pbs.twimg.com/profile_images/511277073319481344/2vsw8AQ7_normal.png"}
• {"id"=>"600199487559176192", "text"=>"#PLOSONE: Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment http://t.co/p4E9k5iYYK", "created_at"=>"2015-05-18T07:21:23Z", "user"=>"Bioecologie", "user_name"=>"Bioecologie", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2718816041/ca2093ca73f3415c0d4b95a761204c11_normal.jpeg"}
• {"id"=>"674932182864011264", "text"=>"#PLOSONE: Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment https://t.co/dLhBsrf3Gd", "created_at"=>"2015-12-10T12:42:26Z", "user"=>"plample_", "user_name"=>"plample", "user_profile_image"=>"http://pbs.twimg.com/profile_images/579720504308793344/8RMVB_8k_normal.jpg"}
• {"id"=>"700070535414341633", "text"=>"Este es el art?culo original de la revista @PLOSONE sobre las 'moscas de la oscuridad'. \nhttps://t.co/4Xp8REF3mH https://t.co/Mj16va1RK4", "created_at"=>"2016-02-17T21:33:16Z", "user"=>"24horas_rne", "user_name"=>"24 horas (RNE)", "user_profile_image"=>"http://pbs.twimg.com/profile_images/441984044184506368/uMSdxpf__normal.jpeg"}
• {"id"=>"700073211195748352", "text"=>"RT @24horas_rne: Este es el art?culo original de la revista @PLOSONE sobre las 'moscas de la oscuridad'. \nhttps://t.co/4Xp8REF3mH https://t…", "created_at"=>"2016-02-17T21:43:54Z", "user"=>"presijabato4", "user_name"=>"Jesus Zamora Rodrigu", "user_profile_image"=>"http://pbs.twimg.com/profile_images/698174721049894912/7Q77hBSW_normal.jpg"}
• {"id"=>"923361107309408256", "text"=>"Have you heard of the Dark Fly? Thanks to Open Access, you can read all about it here: https://t.co/Nd431IMPDL… https://t.co/N1PHsvhgWh", "created_at"=>"2017-10-26T01:30:17Z", "user"=>"Sydney_Library", "user_name"=>"Sydney Uni Library", "user_profile_image"=>"http://pbs.twimg.com/profile_images/603063228273274881/X1OM-iUO_normal.jpg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1476341"], "description"=>"<p>These data represent a summary of our analyses of ROH regions. Homo and hetero SNPs were identified using Samtools and Vcftools functions. The number of homo SNPs was slightly different from that of the fixed SNPs identified using VarScan functions (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone-0033288-t002\" target=\"_blank\">Table 2</a>), due to the difference of data filtering. ROH regions were identified using PLINK software (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s010\" target=\"_blank\">Tables S5</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s011\" target=\"_blank\">S6</a>). The Dark-fly ROH regions showing significantly high homozygosity were determined by statistical analyses (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s012\" target=\"_blank\">Tables S7</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s013\" target=\"_blank\">S8</a>). Genes carrying nsSNPs and cInDels in 21 ROH regions were counted. ND means not determined.</p>", "links"=>[], "tags"=>["roh"], "article_id"=>1008763, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.t003", "stats"=>{"downloads"=>3, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_ROH_regions_/1008763", "title"=>"Identification of ROH regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476340"], "description"=>"<p>These data represent a summary of our analyses of SNPs, InDels and CNVs for the Dark-fly and Oregon-R-S genomes. ND means not determined.</p>", "links"=>[], "tags"=>["indel", "cnv"], "article_id"=>1008762, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.t002", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNP_InDel_and_CNV_analyses_/1008762", "title"=>"SNP, InDel and CNV analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476334"], "description"=>"<p>Mean homozygosity of SNPs in a sliding window (200-kb window at 100-kb steps) was plotted versus the location on 2L (A), 2R (B), 3L (C), 3R (D) and X (E) chromosomes. The Oregon-R-S genome (blue lines) displayed higher homozygosity than the Dark-fly genome (red lines) in most of the regions. Thick horizontal bars represent ROH regions identified by PLINK software for Oregon-R-S (blue bars) and Dark-fly (red bars) and are plotted above the graph without homozygosity values.</p>", "links"=>[], "tags"=>["roh"], "article_id"=>1008756, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g004", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homozygosity_and_ROH_regions_/1008756", "title"=>"Homozygosity and ROH regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476331"], "description"=>"<p>(A) Three-day fecundity (offspring/female) of Dark-fly and Oregon-R-S in LL, LD and DD conditions are shown by box plots. Boxes and median lines represent inter-quartile range and median values of data, and vertical lines represent minimum and maximum values of data within 1.5-fold of the inter-quartile range. Circles indicate values of outliers. * indicates FDR-adjusted p-value<0.05, Welch t-test. n = 10 (total 100 females). (B) Lifetime fecundity (offspring/female) of Dark-fly and Oregon-R-S in LD and DD conditions are shown by box plots in a similar manner to (A). ** indicates p-value<0.01, Welch t-test. n = 10 (total 100 females).</p>", "links"=>[], "tags"=>["dark-fly"], "article_id"=>1008753, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g002", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fecundity_of_Dark_fly_and_Oregon_R_S_/1008753", "title"=>"Fecundity of Dark-fly and Oregon-R-S.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476330"], "description"=>"<p>In 1954, a fly population derived from one pair of Oregon-R-S flies was divided into 6 populations. Three of them (aL, bL and cL populations) were reared in normal light-dark cycling conditions and the remaining three populations (dD, eD, and fD populations) were reared in constant dark conditions. Unfortunately, all of the L lines were lost by 2002. The dD and eD lines were lost in 1965 and 1967, and only the fD line has been maintained until now. In 2008, we started to rear the fD line and designated it “Dark-fly”. We have maintained Dark-fly in a minimum medium as done before (black lines), and in a standard cornmeal medium (white lines) in parallel. The population size of Dark-fly has not been controlled but has usually been about 100 flies each in several culture vials.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>1008752, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_History_of_Dark_fly_/1008752", "title"=>"History of Dark-fly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476350", "https://ndownloader.figshare.com/files/1476351", "https://ndownloader.figshare.com/files/1476352", "https://ndownloader.figshare.com/files/1476353", "https://ndownloader.figshare.com/files/1476354", "https://ndownloader.figshare.com/files/1476355", "https://ndownloader.figshare.com/files/1476356", "https://ndownloader.figshare.com/files/1476357", "https://ndownloader.figshare.com/files/1476358", "https://ndownloader.figshare.com/files/1476359", "https://ndownloader.figshare.com/files/1476360", "https://ndownloader.figshare.com/files/1476361", "https://ndownloader.figshare.com/files/1476362", "https://ndownloader.figshare.com/files/1476363"], "description"=>"<div><p>Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a <i>Drosophila melanogaster</i> line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.</p> </div>", "links"=>[], "tags"=>["genome", "reared"], "article_id"=>1008765, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033288.s001", "https://dx.doi.org/10.1371/journal.pone.0033288.s002", "https://dx.doi.org/10.1371/journal.pone.0033288.s003", "https://dx.doi.org/10.1371/journal.pone.0033288.s004", "https://dx.doi.org/10.1371/journal.pone.0033288.s005", "https://dx.doi.org/10.1371/journal.pone.0033288.s006", "https://dx.doi.org/10.1371/journal.pone.0033288.s007", "https://dx.doi.org/10.1371/journal.pone.0033288.s008", "https://dx.doi.org/10.1371/journal.pone.0033288.s009", "https://dx.doi.org/10.1371/journal.pone.0033288.s010", "https://dx.doi.org/10.1371/journal.pone.0033288.s011", "https://dx.doi.org/10.1371/journal.pone.0033288.s012", "https://dx.doi.org/10.1371/journal.pone.0033288.s013", "https://dx.doi.org/10.1371/journal.pone.0033288.s014"], "stats"=>{"downloads"=>8, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Features_of_Dark_Fly_a_Drosophila_Line_Reared_Long_Term_in_a_Dark_Environment/1008765", "title"=>"Genome Features of “Dark-Fly”, a <i>Drosophila</i> Line Reared Long-Term in a Dark Environment", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476339"], "description"=>"<p>The results of genome sequencing using an Illumina Genome Analyzer II are summarized. Flybase Dmel 5.22 genome (168,736,537 bases) was used as a reference genome.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>1008761, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.t001", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_genome_sequencing_/1008761", "title"=>"Summary of genome sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476337"], "description"=>"<p>A view of Integrated Genomics Viewer around the CG4594 gene. The numerous small gray bars represent reads of genome sequencing. A region of about 500 bases in the CG4594 gene (red thick bar) was not covered by any read sequences of the Dark-fly genome (upper), but was fully covered by the sequences of the Oregon-R-S genome (lower). Numbers on a horizontal line indicate nucleotide position on chromosome 2L. Numbers on vertical alignment indicate read depth.</p>", "links"=>[], "tags"=>["sequences", "cg4594"], "article_id"=>1008759, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_read_sequences_around_CG4594_gene_/1008759", "title"=>"Alignment of read sequences around CG4594 gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476338"], "description"=>"<p>The chromosomal position and length of the Dark-fly ROH regions showing significantly high homozygosity are listed. Genes carrying nsSNPs and InDels in each ROH region are shown. Details regarding nsSNPs and cInDels are presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s004\" target=\"_blank\">File S1</a>.</p>", "links"=>[], "tags"=>["carrying", "nssnps", "cindels", "dark-fly", "roh"], "article_id"=>1008760, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.t004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_carrying_nsSNPs_and_cInDels_in_the_Dark_fly_ROH_regions_/1008760", "title"=>"Genes carrying nsSNPs and cInDels in the Dark-fly ROH regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-14 06:55:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1476332"], "description"=>"<p>The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.</p>", "links"=>[], "tags"=>["curves", "dark-fly"], "article_id"=>1008754, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Survival_curves_of_Dark_fly_and_Oregon_R_S_/1008754", "title"=>"Survival curves of Dark-fly and Oregon-R-S.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime | Further Information

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• {"year"=>2014, "month"=>11, "doi"=>"10.1371/journal.pone.0033288", "f1000_id"=>"14263042", "url"=>"http://f1000.com/prime/14263042", "score"=>1, "classifications"=>["new_finding"], "updated_at"=>"2014-11-24T09:32:31Z"}
• {"year"=>2014, "month"=>12, "doi"=>"10.1371/journal.pone.0033288", "f1000_id"=>"14263042", "url"=>"http://f1000.com/prime/14263042", "score"=>1, "classifications"=>["new_finding"], "updated_at"=>"2014-12-29T09:42:15Z"}
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